Computer Engineering Commons^™

Non-Destructiveapproachto Ellipsometric Monitoring Of A Film Coating On The Inner Surface Of A Tube Shaped Sample, Gregory K. Prilbil, John A. Woollam, Martin M. Liphardt, James D. Welch

Department of Electrical and Computer Engineering: Faculty Publications

Disclosed is the use of a focused electromagnetic beam which is caused to impinge on the top surface of a tube shaped sample, to investigate a film coating on inner surface during fabrication thereof and/or thereafter.

Data Compression Concepts And Algorithms And Their Applications To Bioinformatics, Ozkan U. Nalbantoglu, David J. Russell, Khalid Sayood

Department of Electrical and Computer Engineering: Faculty Publications

Data compression at its base is concerned with how information is organized in data. Understanding this organization can lead to efficient ways of representing the information and hence data compression. In this paper we review the ways in which ideas and approaches fundamental to the theory and practice of data compression have been used in the area of bioinformatics. We look at how basic theoretical ideas from data compression, such as the notions of entropy, mutual information, and complexity have been used for analyzing biological sequences in order to discover hidden patterns, infer phylogenetic relationships between organisms and study viral …

Protein Adsorption On And Swelling Of Polyelectrolyte Brushes: A Simultaneous Ellipsometry-Quartz Crystal Microbalance Study, Eva Bittrich, Keith B. Rodenhausen Jr., Klaus-Jochen Eichhorn, Tino Hofmann, Mathias Schubert, Manfred Stamm, Petra Uhlmann

Department of Electrical and Computer Engineering: Faculty Publications

With a coupled spectroscopic ellipsometry-quartz crystal microbalance with dissipation (QCM-D) experimental setup, quantitative information can be obtained about the amount of buffer components (water molecules and ions) coupled to a poly(acrylic acid) (PAA) brush surface in swelling and protein adsorption processes. PAA Guiselin brushes with more than one anchoring point per single polymer chain were prepared. For the swollen brushes a high amount of buffer was found to be coupled to the brush-solution interface in addition to the content of buffer inside the brush layer. Upon adsorption of bovine serum albumin the further incorporation of buffer molecules into the protein-brush …

Tob1 Is A Constitutively Expressed Repressor Of Liver Regeneration, Karen J. Ho, Nhue L. Do, Hasan H. Otu, Martin J. Dib, Xianghui Ren, Keiichi Enjyoji, Simon C. Robson, Ernest F. Terwilliger, Seth J. Karp

Department of Electrical and Computer Engineering: Faculty Publications

How proliferative and inhibitory signals integrate to control liver regeneration remains poorly understood. A screen for antiproliferative factors repressed after liver injury identified transducer of ErbB2.1 (Tob1), a member of the PC3/BTG1 family of mito-inhibitory molecules as a target for further evaluation. Tob1 protein decreases after 2/3 hepatectomy in mice secondary to posttranscriptional mechanisms. Deletion of Tob1 increases hepatocyte proliferation and accelerates restoration of liver mass after hepatectomy. Down-regulation of Tob1 is required for normal liver regeneration, and Tob1 controls hepatocyte proliferation in a dose-dependent fashion. Tob1 associates directly with both Caf1 and cyclindependent kinase (Cdk) 1 and …

Iterative Signal Processing In Communications, Christian Schlegel, Peter Hoeher, Owe Axelsson, Lance C. Pérez

Department of Electrical and Computer Engineering: Faculty Publications

Iterative signal processing in communications has experienced an explosive rise in popularity in recent years. The catalytic origins of this paradigm-shifting new philosophy among communications experts can be traced to the invention of turbo coding, and the subsequent rediscovery of low-density parity check (LDPC) coding, both in the field of error control coding. Both systems rely on iterative decoding algorithms to achieve their astounding performance. However, iterative signal processing is not confined to the decoding of error control codes and rather quickly spread to many other possible applications. The purpose of this special issue is to examine the concept of …

The Manifestation Of Stopping Sets And Absorbing Sets As Deviations On The Computation Trees Of Ldpc Codes, Eric T. Psota, Lance C. Perez

Department of Electrical and Computer Engineering: Faculty Publications

The error mechanisms of iterative message-passing decoders for low-density parity-check codes are studied. A tutorial review is given of the various graphical structures, including trapping sets, stopping sets, and absorbing sets that are frequently used to characterize the errors observed in simulations of iterative decoding of low-density parity-check codes. The connections between trapping sets and deviations on computation trees are explored in depth using the notion of problematic trapping sets in order to bridge the experimental and analytic approaches to these error mechanisms. A new iterative algorithm for finding low-weight problematic trapping sets is presented and shown to be capable …

Mimo Self-Encoded Spread Spectrum With Iterative Detection Over Rayleigh Fading Channels, Shichuan Ma, Lim Nguyen, Won Mee Jang, Yaoqing (Lamar) Yang

Department of Electrical and Computer Engineering: Faculty Publications

Self-encoded spread spectrum (SESS) is a novel communication technique that derives its spreading code from the randomness of the source stream rather than using conventional pseudorandom noise (PN) code. In this paper, we propose to incorporate SESS in multiple-input multiple-output (MIMO) systems as a means to combat against fading effects in wireless channels. Orthogonal space-time block-coded MIMO technique is employed to achieve spatial diversity, and the inherent temporal diversity in SESS modulation is exploited with iterative detection. Simulation results demonstrate that MIMO-SESS can effectively mitigate the channel fading effect such that the system can achieve a bit error rate of …

Spectroscopicellipsometer And Polarmeter Systemis, John A. Woollam, Blaine D. Johs, Craig M. Herzinger, Ping He, Martin M. Liphardt, Galen L. Pfeiffer

Department of Electrical and Computer Engineering: Faculty Publications

A rotating compensator spectroscopic ellipsometer or polarimeter system having a source of a polychromatic beam of electromagnetic radiation, a polarizer, a stage for Supporting a material system, an analyzer, a dispersive optics and a detector system which comprises a multiplicity of detector elements, the system being functionally present in an environmental control chamber and therefore suitable for application in wide spectral range, (for example, 130-1700 nm). Preferred compensator design involves a Substantially achromatic multiple element compensator systems wherein multiple total internal reflections enter retardance into an entered beam of electromagnetic radiation, and the elements thereof are oriented to minimize changes …

Graphene On Pt(111): Growth And Substrate Interaction, Peter Sutter, Jerzy T. Sadowski, Eli Sutter

Department of Electrical and Computer Engineering: Faculty Publications

In situ low-energy electron microscopy (LEEM) of graphene growth combined with measurements of the graphene structure and electronic band structure has been used to study graphene on Pt (111). Growth by carbon segregation produces macroscopic monolayer graphene domains extending continuously across Pt (111) substrate steps and bounded by strongly faceted edges. LEEM during cooling from the growth temperature shows the propagation of wrinkles in the graphene sheet, driven by thermal stress. The lattice mismatch between graphene and Pt (111) is accommodated by moiré structures with a large number of different rotational variants, without a clear preference for a particular interface …

Scanning Tunneling Microscopy On Epitaxial Bilayer Graphene On Ruthenium (0001), Eli A. Sutter, D.P. Acharya, J.T. Sadowski, P. Sutter

Department of Electrical and Computer Engineering: Faculty Publications

The atomic structure of epitaxial single and bilayer graphene on Ru(0001) was studied by scanning tunneling microscopy (STM). High-resolution imaging of the surface of single layer graphene shows a moiré with pronounced buckling and broken A/B carbon sublayer symmetry due to a strong interaction with the metal substrate. The top sheet of bilayer graphene is largely unperturbed by residual interactions with the substrate. Screened from the metal substrate, it shows the hallmarks of freestanding monolayer graphene: a honeycomb structure with equivalent carbon sublattices imaged in STM and a linear dispersion of bands near the Dirac point.

Automated Ellipsometer And The Like Systems, Blaine D. Johs, Ping He, Martin M. Liphardt, Christopher A. Goeden, John A. Woollam, James D. Welch

Department of Electrical and Computer Engineering: Faculty Publications

Systems and methodology for orienting the tip/tilt and vertical height of samples, preferably automated, as applied in ellipsometer and the like systems.

Automated Ellipsometer And The Like Systems, Blaine D. Johs, Ping He, Martin M. Liphardt, Christopher A. Goeden, Johns A. Woollam, James D. Welch

Department of Electrical and Computer Engineering: Faculty Publications

Systems and methodology for orienting the tip/tilt ad vertical height of samples, preferably automated, as applied in ellipsometer and the like systems

Ground-Plane Quasicloaking For Free Space, Efthymios Kallos, Christos Argyropoulos, Yang Hao

Department of Electrical and Computer Engineering: Faculty Publications

Ground-plane cloak designs are presented, which minimize scattering of electromagnetic radiation from metallic objects in the visible spectrum. It is showed that simplified ground-plane cloaks made from only a few blocks of all-dielectric isotropic materials, either embedded in a background medium or in free space, can provide considerable cloaking performance while maintaining their broadband nature. A design which operates isolated in free space that cloaks radiation originating from a specified direction is also analyzed. These schemes should be much easier to be demonstrated experimentally compared to full designs.

Samplemaskinginellipsometerand The Like Systems Including Detection Of Substrate Backside Reflections, Martin M. Liphardt, James D. Welch, Corey L. Bungay, John A. Woollam

Department of Electrical and Computer Engineering: Faculty Publications

A system and method of preventing substrate backside reflected components in a beam of electromagnetic radiation caused to reflect from the surface of a sample in an ellipsometer or polarimeter system, involving placing a mask adjacent to the surface of the sample which allows electromagnetic radiation to access the sample over only a limited area, wherein to access the sample over only a limited area, wherein the mask can include detector elements for collecting electromagnetic radiation reflected from the sample backside.

Achievable Rates And Resource Allocation Strategies For Imperfectly Known Fading Relay Channels, Junwei Zhang, M. Cenk Gursoy

Department of Electrical and Computer Engineering: Faculty Publications

Achievable rates and resource allocation strategies for imperfectly known fading relay channels are studied. It is assumed that communication starts with the network training phase in which the receivers estimate the fading coefficients. Achievable rate expressions for amplify-and-forward and decode-and-forward relaying schemes with different degrees of cooperation are obtained. We identify efficient strategies in three resource allocation problems: (1) power allocation between data and training symbols, (2) time/bandwidth allocation to the relay, and (3) power allocation between the source and relay in the presence of total power constraints. It is noted that unless the source-relay channel quality is high, cooperation …

Sequencing, Analysis, And Annotation Of Expressed Sequence Tags For Camelus Dromedarius, Abdulaziz M. Al-Swailem, Maher M. Shehata, Faisel M. Abu-Duhier, Essam J. Al-Yamani, Khalid A. Al-Busadah, Mohammed S. Al-Arawi, Ali Y. Al-Khider, Abdullah N. Al-Muhaimeed, Fahad H. Al-Qahtani, Manee M. Manee, Badr M. Al-Shomrani, Saad M. Al-Qhtani, Amer S. Al-Harthi, Kadir C. Akdemir, Mehmet S. Inan, Hasan H. Otu

Department of Electrical and Computer Engineering: Faculty Publications

Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available …

Genes Differentially Expressed By Cumulus Cells And Assays Using Same To Identify Pregnancy Competent Oocytes, Jose B. Cibelli, Amy E. Iager, Hasan H. Otu

Department of Electrical and Computer Engineering: Faculty Publications

A genetic means of identifying "pregnancy competent" oocytes is provided. The means comprises detecting the level of expression of one or more genes that are expressed at characteristic levels (upregulated or downregulated) in cumulus cells derived from pregnancy competent oocytes. This characteristic gene expression level, or pattern referred to herein as the "pregnancy signature", also can be used to identify subjects with underlying conditions that impair or prevent the development of a viable pregnancy, e.g., pre-menopausal condition, other hormonal dysfunction, ovarian dysfunction, ovarian cyst, cancer or other cell proliferation disorder, autoimmune disease and the like. In preferred embodiments the …

Sample Investigating System, Martin M. Liphardt, Thomas E. Tiwald, Blaine D. Johs, Jeffery S. Hale, Craig M. Herzinger, Steven E. Green, Ping He, Ronald A. Synowicki, John A. Woollam

Department of Electrical and Computer Engineering: Faculty Publications

A spectroscopic system for adjusting spacing between an adjacent source/detector as a unit, and a sample, and a reflecting means for directing an incident beam which refelcts from said sample back onto said sample and then into the detector along a locus which is in a plance of incidence that is offset from that of the incident beam, or directly from the reflecting means into the detecor, including means for reducing reflections of a beam fo electromagnetic from the back of a sample, including methodology of use.

Simulation Of Coherent Radar Imaging Using Continuous Wave Noise Radar, Jing Xu, Michael Hoffman, B.L. Cheong, R.D. Palmer

Department of Electrical and Computer Engineering: Faculty Publications

A computationally simple cross-correlation model for multiple backscattering from a continuous wave (CW) noise radar is developed and verified with theoretical analysis and brute-force time-domain simulations. Based on this cross-correlation model, a modification of an existing numerical method originally developed by Holdsworth and Reid for spaced antenna (SA) pulsed radar is used to simulate the estimated cross correlation corresponding to atmospheric backscattering using a coherent CW noise radar. Subse- quently, coherent radar imaging (CRI) processing comparisons between the CW noise radar and a con- ventional pulsed radar are presented that verify the potential of CW noise radar for atmospheric imaging.

Description Of Versatile Optical Polarimetric Scatterometer That Measures All 16 Elements Of The Mueller Matrix For Reflection And Transmission: Application To Measurements Of Scatter Cross Sections, Ellipsometric Parameters, Optical Activity, And The Complex Chiral Parameters, Ezekiel Bahar, Robert D. Kubik

Department of Electrical and Computer Engineering: Faculty Publications

A detailed description of an optical polarimetric scatterometer, its capabilities, and special application are presented. This instrument measures the 44 Mueller matrix elements as well as bidirectional reflective distribution functions scatter cross sectionsfor light that is scattered from a target. Incident polarized light at wavelengths =0.6328 and =1.06 m can be directed toward the target in an arbitrary direction. The receiver can be located anywhere in the solid angle 4. Backscatter measurements, most commonly used in remote sensing, can also be obtained. The scatterometer has been used to validate different analytical/numerical solutions to a broad class of electromagnetic scattering problems, …

Sample Analysis Methodology Utilizngelectromagnetic Radation, John A. Woollam, Corey L. Bungay, Thomas E. Tiwald, Martin M. Liphardt, Ronald A. Synowicki, Gregory K. Pribil, Craig M. Herzinger, Blaine D. Johs, James N. Hilfiker

Department of Electrical and Computer Engineering: Faculty Publications

Simultaneous use of wavelengths in at least two ranges Selected from RADIO, MICRO. FIR, IR, NIR-VIS-NUV. UV, DUV, VUV EUV, XRAY in a regression procedure to evaluate parameters in mathematical dispersion structures to model dielectric functions.

Sample Analysis Methodology Utilizing Electromagnetic Radiation, John A. Woollam, Corey L. Bungay, Thomas E. Tiwald, Martin M. Liphardt, Ronald A. Synowicki, Gregory K. Pribil, Craig M. Herzinger, Blaine D. Johs, James N. Hilfiker

Department of Electrical and Computer Engineering: Faculty Publications

Simultaneous use of wavelengths in at least two ranges selected from RADIO, MICRO, FIR, IR, NIR-VIS-NUV, UV, DUV, VUV, EUV, XRAY in a regression procedure to evaluate parameters in mathematical dispersion structures to model dielectric functions.

System For Reducing Stress Induced Effects Duringdetermination Of Fluid Optical Constants, Thomas E. Tiwald, John A. Woollam, Galen L. Pfeiffer, Blaine D. Johs, Craig M. Herzinger

Department of Electrical and Computer Engineering: Faculty Publications

A system for determination of optical constants of liquids, including provision for reducing stress induced effects while obtaining data.

A Scalable Clustered Camera System For Multiple Object Tracking, Senem Velipasalar, Jason Schlessman, Cheng-Yao Chen, Wayne H. Wolf, Jaswinder P. Singh

Department of Electrical and Computer Engineering: Faculty Publications

Reliable and efficient tracking of objects by multiple cameras is an important and challenging problem, which finds wide-ranging application areas. Most existing systems assume that data from multiple cameras is processed on a single processing unit or by a centralized server. However, these approaches are neither scalable nor fault tolerant. We propose multicamera algorithms that operate on peer-to-peer computing systems. Peer-to-peer vision systems require codesign of image processing and distributed computing algorithms as well as sophisticated communication protocols, which should be carefully designed and verified to avoid deadlocks and other problems. This paper introduces the scalable clustered camera system, which …

Genomic Counter-Stress Changes Induced By The Relaxation Response, Jeffery A. Dusek, Hasan H. Otu, Ann L. Wohlhueter, Manoj Bhasin, Luiz F. Zerbini, Marie G. Joseph, Herbert Benson, Towia A. Libermann

Department of Electrical and Computer Engineering: Faculty Publications

Background: Mind-body practices that elicit the relaxation response (RR) have been used worldwide for millennia to prevent and treat disease. The RR is characterized by decreased oxygen consumption, increased exhaled nitric oxide, and reduced psychological distress. It is believed to be the counterpart of the stress response that exhibits a distinct pattern of physiology and transcriptional profile. We hypothesized that RR elicitation results in characteristic gene expression changes that can be used to measure physiological responses elicited by the RR in an unbiased fashion.

Methods/Principal Findings: We assessed whole blood transcriptional profiles in 19 healthy, long-term practitioners of daily RR …

Proteomic Identification Of Interleukin-2 Therapy Response In Metastatic Renal Cell Cancer, Jon Jones, Hasan H. Otu, Franck Grall, Dimitrios Spentzos, Handan Can, Manuel Aivado, Arie S. Belldegrun, Allan J. Pantuck, Towia A. Libermann

Department of Electrical and Computer Engineering: Faculty Publications

Introduction—To detect a predictive protein profile that distinguishes between IL-2 therapy responders and non-responders among metastatic RCC patients we used surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI TOF-MS).

Materials and Methods—Protein extracts of 56 metastatic clear cell RCC patients obtained from radical nephrectomy specimens and prior to IL-2 therapy were applied to protein chip arrays of different chromatographic properties and analyzed using SELDI TOF-MS. A class prediction algorithm was applied to identify a subset of protein peaks whose expression values were associated with IL-2 response status. Multivariate analysis was performed to assess the association between the proteomic profile …

Differential Expression Of Gadd45Β In Normal And Osteoarthritic Cartilage: Potential Role In Homeostasis Of Articular Chondrocytes, Kosei Ijiri, Luiz F. Zerbini, Haibing Peng, Hasan H. Otu, Kaneyuki Tsuchimochi, Miguel Otero, Cecilia Dragomir, Nicole Walsh, Benjamin E. Bierbaum, David Mattingly, Geoff Van Flandern, Setsuro Komiya, Thomas Aigner, Towia A. Libermann, Mary B. Goldring

Department of Electrical and Computer Engineering: Faculty Publications

Objective—Our previous study suggested that growth arrest and DNA damage–inducible protein 45β (GADD45β) prolonged the survival of hypertrophic chondrocytes in the developing mouse embryo. This study was undertaken, therefore, to investigate whether GADD45β plays a role in adult articular cartilage.

Methods—Gene expression profiles of cartilage from patients with late-stage osteoarthritis (OA) were compared with those from patients with early OA and normal controls in 2 separate microarray analyses. Histologic features of cartilage were graded using the Mankin scale, and GADD45β was localized by immunohistochemistry. Human chondrocytes were transduced with small interfering RNA (siRNA)–GADD45 …

A Theoretical Framework For Quality-Aware Cross-Layer Optimized Wireless Multimedia Communications, Song Ci, Haohong Wang, Dalei Wu

Department of Electrical and Computer Engineering: Faculty Publications

Although cross-layer has been thought as one of themost effective and efficient ways formultimedia communications over wireless networks and a plethora of research has been done in this area, there is still lacking of a rigorous mathematical model to gain indepth understanding of cross-layer design tradeoffs, spanning from application layer to physical layer. As a result, many existing cross-layer designs enhance the performance of certain layers at the price of either introducing side effects to the overall system performance or violating the syntax and semantics of the layered network architecture. Therefore, lacking of a rigorous theoretical study makes existing cross-layer …

Effects Of Wind Field Inhomogeneities On Doppler Beam Swinging Revealed By An Imaging Radar, B.L. Cheong, T.-Y. Yu, Robert D. Palmer, K.-F. Yang, Michael Hoffman, S.J. Frasier, F.J. Lopez-Dekker

Department of Electrical and Computer Engineering: Faculty Publications

In this work, the accuracy of the Doppler beam-swinging (DBS) technique for wind measurements is studied using an imaging radar—the turbulent eddy profiler (TEP) developed by the University of Mas- sachusetts, with data collected in summer 2003. With up to 64 independent receivers, and using coherent radar imaging (CRI), several hundred partially independent beams can be formed simultaneously within the volume defined by the transmit beam. By selecting a subset of these beams, an unprecedented number of DBS configurations with varying zenith angle, azimuth angle, and number of beams can be investigated. The angular distributions of echo power and radial …

Full-Wave Finite-Difference Time-Domain Simulation Of Electromagnetic Cloaking Structures, Yan Zhao, Christos Argyropoulos, Yang Hao

Department of Electrical and Computer Engineering: Faculty Publications

This paper proposes a radial dependent dispersive finitedifference time-domain method for the modeling of electromagnetic cloaking structures. The permittivity and permeability of the cloak are mapped to the Drude dispersion model and taken into account in dispersive FDTD simulations. Numerical simulations demonstrate that under ideal conditions, objects placed inside the cloak are ‘invisible’ to external electromagnetic fields. However for the simplified cloak based on linear transformations, the back scattering has a similar level to the case of a PEC cylinder without any cloak, rendering the object still being ‘visible’. It is also demonstrated numerically that the simplified cloak based on …